[petsc-users] (no subject)

[Li Luo]

Thank you for your reply.

The matrix is small with only 67500 rows, but is relatively dense since a
second-order discontinuous Galerkin FEM is used, nonzeros=23,036,400.
The number of colors is 539 as shown by using -mat_fd_coloring_view:

MatFDColoring Object: 64 MPI processes
  type not yet set
  Error tolerance=1.49012e-08
  Umin=1.49012e-06
  Number of colors=539
  Information for color 0
    Number of columns 1
      378
    Number of rows 756
      0 1188
      1 1188
      2 1188
      3 1188
      4 1188
      5 1188
      ...

Is this normal?
When using MCFD, is there any difference using mpiaij and mpibaij?

Best,
Li

On Mon, Dec 2, 2019 at 10:03 AM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:

>
>   How many colors is it requiring?   And how long is the MatGetColoring()
> taking? Are you running in parallel?  The MatGetColoring() MATCOLORINGSL
> uses a sequential coloring algorithm so if your matrix is large and
> parallel the coloring will take a long time. The parallel colorings are
> MATCOLORINGGREEDY and MATCOLORINGJP
>
>   Barry
>
>
> > On Dec 1, 2019, at 12:56 AM, Li Luo <li.luo at kaust.edu.sa> wrote:
> >
> > Dear Developers,
> >
> > I tried to use the multi-color finite-difference (MC-FD) method for
> constructing the Jacobians. However, I find it is very slow compared to the
> exact Jacobian.
> > My implementation of MC-FD Jacobian is posted below, would you please
> check whether I am correct? Anything missed? Thank you!
> >
> > ////////// Setup phase:
> >           MatStructure flag;
> >           ISColoring   iscoloring;
> >           ierr = MatGetColoring(Jac,MATCOLORINGSL,&iscoloring);
> >           ierr =
> MatFDColoringCreate(Jac,iscoloring,&this->matfdcoloring);
> >           ierr =
> MatFDColoringSetFunction(this->matfdcoloring,(PetscErrorCode
> (*)(void))__libmesh_petsc_snes_residual,(void *)this);
> >           ierr = MatFDColoringSetFromOptions(this->matfdcoloring);
> >           ierr = ISColoringDestroy(&iscoloring);
> >
> > //////////// Apply:
> >           ierr = MatZeroEntries(*jac);CHKERRQ(ierr);
> >           ierr =
> MatFDColoringApply(*jac,solver->matfdcoloring,x,msflag,snes);
> >
> > Best regards,
> > Li Luo
> >
> > This message and its contents, including attachments are intended solely
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>
>

-- 

Postdoctoral Fellow
Extreme Computing Research Center
King Abdullah University of Science & Technology
https://sites.google.com/site/rolyliluo/

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